Marco Pagni

Publication Activity (10 Years)

Years Active: 2000-2021
Publications (10 Years): 5

Top Topics

Metabolic Networks

Chemical Reactions

Gene Expression

Escherichia Coli

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

Sébastien Moretti, T. Van Du Tran, Florence Mehl, Mark Ibberson, Marco Pagni
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models. Nucleic Acids Res. 49 (Database-Issue) (2021)
Nurgazy Sulaimanov, Sunil Kumar, Frédéric Burdet, Mark Ibberson, Marco Pagni, Heinz Koeppl
Inferring gene expression networks with hubs using a degree weighted Lasso approach. Bioinform. 35 (6) (2019)
T. Van Du Tran, Sébastien Moretti, Alix T. Coste, Sara Amorim-Vaz, Dominique Sanglard, Marco Pagni
Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis. Bioinform. 35 (13) (2019)
Anne Morgat, Thierry Lombardot, Kristian B. Axelsen, Lucila Aimo, Anne Niknejad, Nevila Hyka-Nouspikel, Elisabeth Coudert, Monica Pozzato, Marco Pagni, Sébastien Moretti, Steven Rosanoff, Joseph Onwubiko, Lydie Bougueleret, Ioannis Xenarios, Nicole Redaschi, Alan Bridge
Updates in Rhea - an expert curated resource of biochemical reactions. Nucleic Acids Res. 45 (Database-Issue) (2017)
Sébastien Moretti, Olivier Martin, T. Van Du Tran, Alan Bridge, Anne Morgat, Marco Pagni
MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. Nucleic Acids Res. 44 (Database-Issue) (2016)
Thomas Bernard, Alan Bridge, Anne Morgat, Sébastien Moretti, Ioannis Xenarios, Marco Pagni
Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings Bioinform. 15 (1) (2014)
Marco Pagni, Hélène Niculita-Hirzel, Loïc Pellissier, Anne Dubuis, Ioannis Xenarios, Antoine Guisan, Ian R. Sanders, Jérôme Goudet, Nicolas Guex
Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1. Bioinform. 29 (10) (2013)
Thierry Schüpbach, Marco Pagni, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios, Lorenzo Cerutti
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles. Bioinform. 29 (9) (2013)
Mathias Ganter, Thomas Bernard, Sébastien Moretti, Jörg Stelling, Marco Pagni
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. Bioinform. 29 (6) (2013)
Guido Bologna, Anne-Lise Veuthey, Marco Pagni, Lydie Lane, Amos Bairoch
A Preliminary Study on the Prediction of Human Protein Functions. IWINAC (1) (2011)
Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, Jacques Rougemont
The Microbe browser for comparative genomics. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Heinz Stockinger, Teresa K. Attwood, Shahid Nadeem Chohan, Richard G. Côté, Philippe Cudré-Mauroux, Laurent Falquet, Pedro L. Fernandes, Robert D. Finn, Taavi Hupponen, Eija Korpelainen, Alberto Labarga, Aurélie Laugraud, Tania Lima, Evangelos Pafilis, Marco Pagni, Steve Pettifer, Isabelle Phan, Nazim Rahman
Experience using web services for biological sequence analysis. Briefings Bioinform. 9 (6) (2008)
Marco Pagni, Jörg Hau, Heinz Stockinger
A Multi-protocol Bioinformatics Web Service: Use SOAP, Take a REST or Go with HTML. CCGRID (2008)
Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Jörg Hau, Olivier Martin, Dmitri Kuznetsov, Laurent Falquet
MyHits: improvements to an interactive resource for analyzing protein sequences. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Jörg Hau, Michael Muller, Marco Pagni
HitKeeper, a generic software package for hit list management. Source Code Biol. Medicine 2 (2007)
Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Marco Pagni, Christian J. A. Sigrist
The PROSITE database. Nucleic Acids Res. 34 (Database-Issue) (2006)
Heinz Stockinger, Marco Pagni, Lorenzo Cerutti, Laurent Falquet
Grid Approach to Embarrassingly Parallel CPU-Intensive Bioinformatics Problems. e-Science (2006)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex L. Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu
InterPro, progress and status in 2005. Nucleic Acids Res. 33 (Database-Issue) (2005)
Peter Sperisen, Marco Pagni
JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture. BMC Bioinform. 6 (2005)
Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Laurent Falquet
MyHits: a new interactive resource for protein annotation and domain identification. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, C. Victor Jongeneel
trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Res. 32 (Database-Issue) (2004)
Alexandre Gattiker, Karine Michoud, Catherine Rivoire, Andrea H. Auchincloss, Elisabeth Coudert, Tania Lima, Paul J. Kersey, Marco Pagni, Christian J. A. Sigrist, Corinne Lachaize, Anne-Lise Veuthey, Elisabeth Gasteiger, Amos Bairoch
Automated annotation of microbial proteomes in SWISS-PROT. Comput. Biol. Chem. 27 (1) (2003)
Laurent Falquet, Lorenza Bordoli, Vassilios Ioannidis, Marco Pagni, C. Victor Jongeneel
Swiss EMBnet node web server. Nucleic Acids Res. 31 (13) (2003)
Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, Evgeni M. Zdobnov
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31 (1) (2003)
Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Sam Griffiths-Jones, Daniel H. Haft, Henning Hermjakob, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, Sue Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Florence Servant, Christian J. A. Sigrist
InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites Briefings Bioinform. 3 (3) (2002)
Christian J. A. Sigrist, Lorenzo Cerutti, Nicolas Hulo, Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher
PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors. Briefings Bioinform. 3 (3) (2002)
Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J. A. Sigrist, Kay Hofmann, Amos Bairoch
The PROSITE database, its status in 2002. Nucleic Acids Res. 30 (1) (2002)
Thomas Junier, Marco Pagni, Philipp Bucher
mmsearch: a motif arrangement language and search program. Bioinform. 17 (12) (2001)
Marco Pagni, Christian Iseli, Thomas Junier, Laurent Falquet, C. Victor Jongeneel, Philipp Bucher
trEST, trGEN and Hits: access to databases of predicted protein sequences. Nucleic Acids Res. 29 (1) (2001)
Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov
The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29 (1) (2001)
Marco Pagni, C. Victor Jongeneel
Making Sense of Score Statistics for Sequence Alignments. Briefings Bioinform. 2 (1) (2001)
Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov
InterPro-an integrated documentation resource for protein families, domains and functional sites. Bioinform. 16 (12) (2000)
Thomas Junier, Marco Pagni
Dotlet: diagonal plots in a Web browser. Bioinform. 16 (2) (2000)